[EMBOSS] can't access databases indexed by dbifasta

[David Martin]

On 17/2/04 3:23 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:

> Hi,
> 
> I have now changed emboss/emboss.defaults to:
> 
> SET $emboss_db_dir /var/data/blast_db
> 
> DB ecoli.nt [
>  type: "N"
>  format: "fasta"
>  method: "emblcd"
>  dir: "$emboss_db_dir"
>  indexdir: "$emboss_db_dir"
>  file: "ecoli.nt"
> ]
> 
> And get the same negative result:
> 
> [marcus]$ showdb
> Displays information on the currently available databases
> # Name        Type ID  Qry All Comment
> # ====        ==== ==  === === =======
> ecoli.nt      N    OK  OK  OK  -
> 
> [marcus]$ seqret ecoli.nt

'seqret ecoli.nt:\*' perhaps?

..d

> Reads and writes (returns) sequences
> Error: failed to open filename 'ecoli.nt'
> Error: Unable to read sequence 'ecoli.nt'
> Died: seqret terminated: Bad value for '-sequence' and no prompt
> 
> I find this very strange! If you don't know what's wrong would you know
> anywhere else I can get help with this?
> 
> Thanks again.
> 
> Marcus
> 
> 
> On Tue, 2004-02-17 at 15:07, David Martin wrote:
>> On 17/2/04 2:49 pm, "Marcus Claesson" <m.claesson at student.ucc.ie> wrote:
>> 
>>> Thanks for your answer Jerome! But it didn't seem to help me. I added
>>> the indexdir line with the same path (where the index files and fasta
>>> file is) as "dir:". I tried this both with and without setting a
>>> emboss_db_dir variable, but it still didn't work. In other words I can
>>> still only access the database (that shows up in showdb) if I am in that
>>> fasta file directory.
>> 
>> This is because you have not set the file: option? try that and see if it
>> works.
>> in the original example you give the database the same name as the fasta
>> file so it works if it is in the right directory.
>> 
>>> 
>>> Do I need to set this path somewhere else than in emboss.default you
>>> think?
>> 
>>>> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
>>>> 
>>>> 
>>>> DB rbcl [
>>>>     type: N
>>>>     method: emblcd
>>>>     format: fasta
>>>>     dir: $jerome_database_dir/banque1
>>>>     indexdir: $jerome_database_dir/banque1
>>        file: seqfile.fasta
>>        comment: "It is useful to put a description here"
>>>> ]
>> 
>> 
>> ..d
> 
>